The long term goal of this work is to develop lower cost analytical instrumentation and the associated analytical methodology for improved structure determination of biomolecules. Matrix-assisted laser desorption ionization (MALDI) will be combined with a quadrupole ion trap. The MALDI technique appears to have a number of characteristics that will make it superior to the standard method ionization method for biological molecules in use today, Fast Atom Bombardment (FAB). MALDI has the potential to have significantly better sensitivity than FAB, is less prone to matrix/sample incompatibilities, and produces significantly less chemical noise in the mass spectrum. The quadrupole ion trap has become well known for its sensitivity and MS/MS capabilities and thus the combination of it with MALDI should offer tremendous potential. In addition to optimizing the interface of MALDI with the ion trap, work will be performed to better understand the physico-chemical aspects of MS/MS of ions from biological molecules.